[gmx-users] error ffg53a

Justin A. Lemkul jalemkul at vt.edu
Wed Aug 27 17:45:06 CEST 2008

shahrbanoo karbalaee wrote:
> Dear justin
> as you wrote, the first I make tfe.topology  with this force field  by
> command pdb2gmx and pdbfile from prodrg.and add to box with spc.now I
> have the file spc and tfe.by command grommp I minimized this file .I
> got a file emsolve.after this  ,I work  on this peptide .
> pdb2gmx -f  name  -ter -ignh
> editconf                -d 0.7
> genbox -cp box.gro -cs emsolve.gro -p 1vm52.top -o solvated.gro
> grompp -f em.mdp -p 1vm52.top -c solvated.gro -o em.tpr
> I thought the program read from tfe.itp in /share/top file then I
> rename it and add  the tfe.itp is made by drg.but it isnot right.and
> els I add  gd_20 to tfe.itp because the program got error this
> line.and gd_29 in 1vm52.top .

Now I see.  The tfe.itp in /share/top uses ffgmx atom types and parameters, 
hence why you are seeing 'HO,' which corresponds to the hydrogen of a hydroxyl 
group.  In your topology, you call "tfe.itp," but the tfe.itp that you posted 
contains only position restraint information.

What you will want to do is the following:

1. Use the parameters from tfe.top that you posted, removing the force field 
call and [ system ] and [ molecules ] sections, as well as any other #include 
statements for things like spc.itp or whatever else.  Rename this file something 
like "my_tfe.itp"

2. Use #include "my_tfe.itp" in your system topology that contains your protein.


> best
> sh-karbalaee
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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